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accession-icon SRP076450
Drosophila melanogaster (fruit fly) Head, Testis and Ovary Transcriptome RNA-seq
  • organism-icon Drosophila melanogaster
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

We sequenced DGRP (Drosophila Genetic Reference Panel) line 208 for strand-specific RNA-seq in head, testis and ovary. The RNA-seq (2x150bp) data is intended to investigate the expression profiles of polymorphic duplications and de novo gene, as well as other lncRNAs.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon SRP053641
Danio rerio Transcriptome or Gene expression
  • organism-icon Danio rerio
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

To investigate the transcriptional regulation in zebrafish liver during the process of regeneration after 1/9 PH

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP017563
Zebrafish larvae exposed to cold or hypoxia stress
  • organism-icon Danio rerio
  • sample-icon 17 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses, larvae at 96hpf were exposed to cold stress (16 Celsius degree) or hypoxia (5% O2) for 24h, and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. After environmental exposure, RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP053395
Danio rerio Transcriptome or Gene expression
  • organism-icon Danio rerio
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

To investigate the transcriptional regulation in zebrafish liver during the process of regeneration after 1/3 PH

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP077477
Control stress dataset for transcriptomic developmental map of Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 28 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Arabidopsis thaliana is a main model species for plant science, especially for such branches as molecular biology, genetics and genomics. We present here first genome-wide analysis of expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing (RNA-seq). To determine whether the developmental map represented the majority of the expressed genes, we analyzed gene expression under various abiotic stress conditions.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon SRP050133
RNA-seq Analysis of an Apical Meristem Time Series Reveals a Critical Point in Arabidopsis thaliana Flower Initiation
  • organism-icon Arabidopsis thaliana
  • sample-icon 26 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been described. In this study we analyzed gene expression during Arabidopsis thaliana meristem development from day 7 to 16 after germination in one-day increments. The dynamics of the expression of the main flowering regulators were consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. GO enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle, suggesting that during transition to the flowering stage a change in dynamics of cell division takes place. In particular, we hypothesize that a subset of the meristematic cells experiences a forced exit from G0 at day 10. Finally, we observed an acceleration of the cell cycle at day 11, which may be linked to meristem reorganization preceding activation of LFY.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP043021
Tumor suppressor p53 antagonizes Activating Transcription Factor 4-mediated gene expression in response to mitochondrial respiration chain complex III inhibition
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Human cell line HCT116 incubated with Myxothiazol for 5 or 17 hours

Publication Title

A sustained deficiency of mitochondrial respiratory complex III induces an apoptotic cell death through the p53-mediated inhibition of pro-survival activities of the activating transcription factor 4.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP079984
Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B-cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

RNA-Seq of EBV-positive B-lymphoblastoid cell line MP1 and EBV-positive Burkitt’s lymphoma cell line Raji

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

View Samples
accession-icon E-MTAB-925
Transcription profiling by array of the hypothlamus and thalamus of the offspring of chickens exposed to acute stress at an early age
  • organism-icon Gallus gallus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The data for the parental stressed and control birds is available in ArrayExpress with accession E-MTAB-924, while this experiment only concerns their offspring that never been exposed to early life stress.

Publication Title

Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Treatment

View Samples
accession-icon E-AFMX-1
Transcription profiling of human, chimp and mouse brain
  • organism-icon Macaca mulatta, Mus caroli, Mus musculus, Pan troglodytes, Pongo pygmaeus, Homo sapiens, Mus spretus
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Human Genome U95 Version 2 Array (hgu95av2)

Description

Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.

Publication Title

A neutral model of transcriptome evolution.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

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...

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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